2ey4

Crystal Structure of a Cbf5-Nop10-Gar1 Complex

Method: X-RAY DIFFRACTION D_max: 136.6 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2ey4
沉积日期 deposition_date	2005-11-09
结构标题 title	Crystal Structure of a Cbf5-Nop10-Gar1 Complex
关键词 keywords	;Trimeric complex, Structural Genomics, PSI, Protein Structure Initiative, Southeast Collaboratory for Structural Genomics, SECSG, ISOMERASE-BIOSYNTHETIC PROTEIN COMPLEX ;; ISOMERASE/BIOSYNTHETIC PROTEIN
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	41.35 Å
回转半径 Rg (电子) rg_electron	41.41 Å
零角强度 I(0) i0	147971000.00
分子量 molecular_weight	103430.0 kDa
排除体积 excluded_volume	131670 Å³
包络体积 envelope_volume	180900 Å³
水化壳体积 shell_volume	39074 Å³
包络直径 envelope_diameter	140.4 Å
壳层 Rg shell_rg	43.10 Å
包络 Rg envelope_rg	40.49 Å
形状 Rg shape_rg	41.41 Å
总 Rg total_rg	41.52 Å
总原子数 total_atoms	7280
残基数 n_residues	907
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	136.6 Å
Rg (实空间) rg_real	41.57 Å
Rg 误差 (实空间) rg_real_error	1.33 Å
I(0) (实空间) i0_real	1.4800e+08
I(0) 误差 (实空间) i0_real_error	2.5820e+06
Rg (倒空间) rg_reciprocal	41.35 Å
I(0) (倒空间) i0_reciprocal	147900000.0000
解质量估计 total_estimate	0.8448
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	32.4 Å
偏度 Skewness skewness	0.349
峰度 Kurtosis kurtosis	-0.710
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	10470000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.860; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.809; Smooth: 0.590

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (5)

Entity 1 polymer

描述 description	Probable tRNA pseudouridine synthase B
分子量 formula_weight	37664.0 kDa
EC 编号 ec_number	5.4.99.-
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	7456

MARDEVRRILPADIKREVLIKDENAETNPDWGFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPVALEKATRVVQALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRLRTRKVYYIEVLEIEGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMSELRRTRSGPFKEDETLITLHDLVDYYYFWKEDGIEEYFRKAIQPMEKAVEHLPKVWIKDSAVAAVTHGADLAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEMLEKTKGIAVDVEKVFMPRDWYPKL

来源 Source

来源生物 organism	Pyrococcus furiosus
NCBI 分类编号 ncbi_taxonomy_id	2261
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	small nucleolar rnp similar to gar1
分子量 formula_weight	9505.3 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,D

MEKQGEKMKRLGKVLHYAKQGFLIVRTNWVPSLNDRVVDKRLQFVGIVKDVFGPVKMPYVAIKPKVSNPEIYVGEVLYVDER

来源 Source

来源生物 organism	Pyrococcus furiosus
NCBI 分类编号 ncbi_taxonomy_id	186497
宿主生物 host_organism	Escherichia coli

Entity 3 polymer

描述 description	Ribosome biogenesis protein Nop10
分子量 formula_weight	6640.9 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	E,F

MRFRIRKCPKCGRYTLKEVCPVCGEKTKVAHPPRFSPEDPYGEYRRRWKREVLGI

来源 Source

来源生物 organism	Pyrococcus furiosus
NCBI 分类编号 ncbi_taxonomy_id	2261
宿主生物 host_organism	Escherichia coli

Entity 4 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	176

▼

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d2ey4a1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.122 — PUA domain-like
超家族 Superfamily superfamily	b.122.1 — PUA domain-like
家族 Family family	b.122.1.1 — PUA domain

结构域编号 domain_id	d2ey4a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.265 — Pseudouridine synthase
超家族 Superfamily superfamily	d.265.1 — Pseudouridine synthase
家族 Family family	d.265.1.2 — Pseudouridine synthase II TruB

结构域编号 domain_id	d2ey4b1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.122 — PUA domain-like
超家族 Superfamily superfamily	b.122.1 — PUA domain-like
家族 Family family	b.122.1.1 — PUA domain

结构域编号 domain_id	d2ey4b2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.265 — Pseudouridine synthase
超家族 Superfamily superfamily	d.265.1 — Pseudouridine synthase
家族 Family family	d.265.1.2 — Pseudouridine synthase II TruB

结构域编号 domain_id	d2ey4c1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
超家族 Superfamily superfamily	b.43.3 — Translation proteins
家族 Family family	b.43.3.5 — Gar1-like SnoRNP

结构域编号 domain_id	d2ey4d_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
超家族 Superfamily superfamily	b.43.3 — Translation proteins
家族 Family family	b.43.3.5 — Gar1-like SnoRNP

结构域编号 domain_id	d2ey4e1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.41 — Rubredoxin-like
超家族 Superfamily superfamily	g.41.16 — Nop10-like SnoRNP
家族 Family family	g.41.16.1 — Nucleolar RNA-binding protein Nop10-like

结构域编号 domain_id	d2ey4f_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.41 — Rubredoxin-like
超家族 Superfamily superfamily	g.41.16 — Nop10-like SnoRNP
家族 Family family	g.41.16.1 — Nucleolar RNA-binding protein Nop10-like

CATH v4.4 (8 domains)

结构域编号 domain_id	2ey4A01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	130 — Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4
同源超家族 H-superfamily homologous superfamily	10 — PUA domain

结构域编号 domain_id	2ey4A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	2350 — Pseudouridine synthase
同源超家族 H-superfamily homologous superfamily	10 — Pseudouridine synthase

结构域编号 domain_id	2ey4B01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	130 — Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4
同源超家族 H-superfamily homologous superfamily	10 — PUA domain

结构域编号 domain_id	2ey4B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	2350 — Pseudouridine synthase
同源超家族 H-superfamily homologous superfamily	10 — Pseudouridine synthase

结构域编号 domain_id	2ey4C00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily	230 — Probable tRNA pseudouridine synthase domain

结构域编号 domain_id	2ey4D00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily	230 — Probable tRNA pseudouridine synthase domain

结构域编号 domain_id	2ey4E00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	28 — Rubrerythrin, domain 2
同源超家族 H-superfamily homologous superfamily	40 — H/ACA ribonucleoprotein complex, subunit Nop10

结构域编号 domain_id	2ey4F00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	20 — Single Sheet
拓扑 Topology topology	28 — Rubrerythrin, domain 2
同源超家族 H-superfamily homologous superfamily	40 — H/ACA ribonucleoprotein complex, subunit Nop10

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	36.087 Å
晶胞边长 b length_b	75.361 Å
晶胞边长 c length_c	103.240 Å
晶胞夹角 α angle_alpha	95.90 °
晶胞夹角 β angle_beta	96.90 °
晶胞夹角 γ angle_gamma	94.99 °
晶胞分子数 Z z_pdb	2

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	2.110 Å
最低分辨率 resolution_low	39.970 Å
R 因子 r_factor	0.2110
R_work r_work	0.2110
R_free r_free	0.2550

fit	/app/data/saxs_computation/ey/2ey4/2ey4.fit
pddf	/app/data/pr_computation/ey/2ey4/2ey4.pr.out
profile	/app/data/saxs_computation/ey/2ey4/2ey4.dat

Crystal Structure of a Cbf5-Nop10-Gar1 Complex

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

5. 实体与聚合体信息 (5)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)